Biology subjects

Farrell, A. P.

Publications and source records attributed to Farrell, A. P..

3 recordsLinked to original sources

bioRxiv2025

A decision matrix to better identify repeatable physiological variation within individuals

The performance of an individual has remained at the heart of evolutionary biology since the time of Darwin. Physiologists are equally drawn to the implications of individual variation for health and sporting endeavours, and specifically, whether or not a physiological trait is repeatable within an individual. Experimental biologists are especially interested in temporally stable physiological traits that are relevant to an individuals lifetime fitness for natural selection to act upon. Experimental noise, however, confounds the measurement of such repeatability, even though validated protocols exist for measuring many meaningful physiological performance traits. Missing is a decision matrix that helps distinguish individual variation from experimental noise. We propose a precision-&-repeatability assessment matrix (PRAM) that integrates established assessments of individual variability and repeatability. This matrix places metrics that are more repeatable and precise in the quadrant closest to the origins of Cartesian coordinates; those farthest away are less acceptable in terms of both repeatability and precision. As a case study, PRAM is applied to whole-organism aerobic and non-aerobic metabolic performance metrics from fish that were measured with the same protocols. The analysis illustrates that aerobic metabolic metrics can be more repeatable and precise than non-aerobic ones. Consequently, PRAM helps physiologists to better understand whether the observed variability is due to non-repeatable metrics or true individual variation.

physiology↗

bioRxiv2018

Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity, temperature, but not dissolved oxygen

An organisms ability to respond effectively to environmental change is critical to their survival. Yet, life stage and overall condition can dictate tolerance thresholds to heightened environmental stressors, such that stress may not be equally felt across individuals within a species. Environmental changes can induce transcriptional responses in an organism, some of which reflect generalized responses, and others are highly specific to the type of change being experienced. Thus, if transcriptional biomarkers specific to a heightened environmental stressor, even under multi-stressor impacts, can be identified, the biomarkers could be then applied in natural environments to determine when and where individuals are experiencing such stressors. Here, we validate candidate gill gene expression biomarkers by experimentally challenging juvenile Chinook salmon (Oncorhynchus tshawytscha). A sophisticated experimental set-up (four trials) manipulated salinity (freshwater, brackish water, and seawater), temperature (10, 14, and 18{degrees}C), and dissolved oxygen (normoxia and hypoxia), in all 18 possible combinations, for up to six days during the pre-smolt, smolt, and de-smolt life stages. In addition, we also describe the changes in juvenile behaviour, plasma variables, gill Na+/K+- ATPase (NKA) activity, body size, body morphology, and skin pigmentation associated with salinity, temperature, dissolved oxygen, mortality, and smolt status. We statistically identified biomarkers specific to salinity and temperature treatments, as well as mortality across multiple stressors and life stages. Similar biomarkers for the dissolved oxygen treatment could not be identified in the data and we discuss our next steps using an RNA-seq study. This work demonstrates the unique power of gene expression biomarkers to identify a specific stressor even under multi-stressor conditions.

genomics↗

bioRxiv2018

Discovery and validation of candidate smoltification gene expression biomarkers across multiple species and ecotypes of Pacific salmonids

Early marine survival of juvenile salmon is intimately associated with their physiological condition during ocean entry and especially smoltification. Smoltification is a developmental parr-smolt transformation allowing salmon to acquire the trait of seawater tolerance in preparation for marine living. Traditionally, this developmental process has been monitored using gill Na+/K+ATPase (NKA) activity or plasma hormones, but gill gene expression can be reliably used. Here, we describe the discovery of candidate genes from gill tissue for staging smoltification using comparisons of microarray studies with particular focus on the commonalities between anadromous Rainbow trout and Sockeye salmon datasets, as well as literature comparison encompassing more species. A subset of 37 candidate genes mainly from the microarray analyses was used for Taq-Man qPCR assay design and their monthly expression patterns were validated using gill samples from four groups, representing three species and two ecotypes: Coho salmon, Sockeye salmon, stream-type Chinook salmon, and ocean-type Chinook salmon. The best smoltification biomarkers, as measured by consistent changes across these four groups, were genes involved in ion regulation, oxygen transport, and immunity. Smoltification gene expression patterns (using the top 10 biomarkers) were confirmed by significant correlations with NKA activity and were associated with changes in body brightness, caudal fin darkness, and caudal peduncle length. We incorporate gene expression patterns of pre-smolt, smolt, and de-smolt trials from acute seawater transfers using a companion study to develop a preliminary seawater tolerance classification model for ocean-type Chinook salmon. This work demonstrates the potential of gene expression biomarkers to stage smoltification and classify juveniles as pre-smolt, smolt, or de-smolt.

genomics↗